EMERSE Community Meeting

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This document provides an overview of the EMERSE Community Meeting held on October 1, 2024. The meeting included welcome messages, system demos, open forums, acknowledgements, research collaborative details, publications, and more. Learn about the community engagement, research focus, collaborative contributions, and recent publications shared during the meeting.

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EMERSE Community Meeting 2024-Oct-01 https://project-emerse.org https://project-emerse.org

Plan for today Welcome and Housekeeping Announcements and Updates Brief System Demo Open Forum Adjourn

Housekeeping Zoom Meeting More opportunities for interaction Please stay muted, unless you would like to ask a question or make a comment Feel free to use the chat function to type questions or provide comments We will answer questions throughout We will record this meeting; it will be available where prior recordings are located: https://project-emerse.org/presentations.html https://project-emerse.org/community.html

Community https://project-emerse.org/community.html

Acknowledgements EMERSE has been supported by: NCI ITCR program NCATS via MICHR CTSA Michigan Medicine Department of Learning Health Sciences Office of Research Health Information Technology & Services

Research Collaborative Initialresearchfocus: pronoun usage in the EHR over time Contributions from U Michigan, UCSF, U Virginia, U Cincinnati, U Iowa Abstract will be presented at November 2024 AMIA Symposium in SF Next steps: poster, paper, and new projects Ifinterested inparticipating, pleasecontact EMERSE-team@umich.edu

Publications https://project-emerse.org/publications.html

Publications (new since last meeting) Derstine BA, Holcombe SA, Wang NC, Ross BE, Sullivan JA, Wang SC, Su GL. Relative muscle indices and healthy reference values for sarcopenia assessment using T10 through L5 computed tomography skeletal muscle area. Sci Rep. 2024 Sep 18;14(1):21799. doi: 10.1038/s41598-024-71613-x. PMCID: PMC11410951. PMID: 39294201 StabelliniN, Cullen J, Bittencourt MS, Moore JX, Sutton A, Nain P, HamerschlakN, Weintraub NL, Dent S, Tsai MH, Banerjee A, Ghosh AK, Sadler D, Coughlin SS, Barac A, Shanahan J, Montero AJ, Guha A. Allostatic Load/Chronic Stress and Cardiovascular Outcomes in Patients Diagnosed With Breast, Lung, or Colorectal Cancer. J Am Heart Assoc. 2024 Jul 16;13(14):e033295. doi: 10.1161/JAHA.123.033295. Epub 2024 Jul 9. PMCID: PMC11292743. PMID: 38979791 Mohan A, Quingalahua E, Gunchick V, Paul S, Kumar-Sinha C, Crysler O, Zalupski MM, Sahai V. PARP inhibitor therapy in patients with IDH1 mutated cholangiocarcinoma. Oncologist. 2024 Aug 5;29(8):725-730. doi: 10.1093/oncolo/oyae163. PMCID: PMC11299928. PMID: 39036962 Ahmed M, Pu A, Jencks K, Bishu S, Higgins P, Chey WD, Rao K, Lee A. Predictors of irritable bowel syndrome-like symptoms in quiescent inflammatory bowel disease. NeurogastroenterolMotil. 2024 Jun;36(6):e14809. doi: 10.1111/nmo.14809. Epub 2024 Apr 23. PMID: 38651743 Owlett LD, Zapanta B, Sandkuhler SE, Ames EG, Hickey SE, Mackenzie SJ, Meisner JK. Multicenter appraisal of comorbid TANGO2 deficiency disorder in patients with 22q11.2 deletion syndrome. Am J Med Genet A. 2024 Jun 3:e63778. doi: 10.1002/ajmg.a.63778. Epub ahead of print. PMID: 38829177 Huppert LA, Fisch S, TsopurashviliE, SomepalleSS, Salans M, Vasudevan HN, Jo Chien A, Majure M, Rugo HS, BalassanianR, Boreta L, MeliskoME. Demographic and clinical characteristics of patients with metastatic breast cancer and leptomeningeal disease: a single center retrospective cohort study. Breast Cancer Res Treat. 2024 Jun 18. doi: 10.1007/s10549-024-07339-1. Epub ahead of print. PMID: 38888796 Shabet C, KattapuramM, Burton A, Thoeny R, Nielsen H, Accardo ML, Smith EH, Koeppe E, Else T, Cha KB. A retrospective cohort study of genetic referral and diagnosis of Birt-Hogg-Dub Syndrome in patients with Trichodiscomaand Fibrofolliculoma skin lesions. Fam Cancer. 2024 Jun 1. doi: 10.1007/s10689-024-00402-2. Epub ahead of print. PMID: 38822938 Sabharwal B, Lawal NO, Smith MA. Rotating Palliative Care Patients From Full Agonist Opioids to Low Dose Milligram Buprenorphine. J Pain Symptom Manage. 2024 May 21:S0885- 3924(24)00786-3. doi: 10.1016/j.jpainsymman.2024.05.018. Epub ahead of print. PMID: 38777074 Carrasco M, EstiphanT, McCaffery H, McNamara N. "Is it a seizure?" Prediction tool for seizure likelihood in children aged 1-24 months admitted for electroencephalographic monitoring of paroxysmal, rhythmic, and repetitive events. Epilepsia. 2024 May 29. doi: 10.1111/epi.18018. Epub ahead of print. PMID: 38808646 Ahn AB, Kulhari S, Rhee J, Cooper G. Inappropriate Ordering of Multitarget Stool DNA Tests for Colon Cancer Screening. J Am Board Fam Med. 2024 Mar-Apr;37(2):328-331. doi: 10.3122/jabfm.2023.230164R2. PMID: 38740492

Publications - quotation A retrospective cohort was obtained through use of...EMERSE...Cohort 1 contained one previously diagnosed patient with comorbid 22q11.2DS and TDD, and this patient was identified as high risk using this screening system and demonstrated the efficacy of the screening methodology. [PMID 38829177]

Imminent software release Version 7 Has been in production at U of Michigan ~1 month External Release date: We re getting really, really close! Mostly documentation updates and minor bug fixes Some documentation components have been re-written and re- organized to make them more clear

Updating to version 7 Moderate complexity But less than install, since not dealing with DB compatibility, etc. We will work with sites individually on the upgrade Must upgrade from version-to-version, don t skip steps contact us when you are ready or want to discuss logistics Reindexing is necessary index is restructured to handle NLP Multiple new components, new DB tables, etc

Updating to version 7 Someone at your site will need an active UMLS license https://www.nlm.nih.gov/databases/umls.html Not required or expected of standard users We will provide a UMLS extract We will provide a new synonyms file to map terms to UMLS CUIs Need to update user search terms Prior systems lacked robust validation We will provide scripts looks for things that cannot be automatically fixed

Updating to version 7 NLP is built-in Named entity recognition (NER) diagnoses, procedures, drugs, etc. Attributes negation, uncertainty, subject, history of Negation, Uncertainty, etc, based on sets of regular expressions/patterns Everything possible is tagged with attributes, not just UMLS concepts possible rain showers for the Michigan game Sentence/phrase detection is challenging in notes If you don t like the built-in NLP you can use your own system and add annotations at the time of indexing We have documentation on how to do this We can meet to discuss/plan

Example custom NLP header RU1FUlNFX0g=2|5|XHRcdEVNRVJTRSoqKioqKioqRVNSRU1FXHRcdA== 800 810 CUI_0015392R 800 810 SMG_ANATOMY 1169 1173 CUI_0023317R 1169 1173 SMG_ANATOMY 1580 1590 CUI_0015392R 1580 1590 SMG_ANATOMY 1672 1675 CUI_0015392R R R R ... 1971 1971 1971 5528 5528 5528 XHRcdEVNRVJTRSoqKioqKioqRVNSRU1FXHRcdA== Case Report from the Journal of Medical Case Reports 1983 1983 1983 5535 5535 5535 POL_NEG CUI_0025952R SMG_TITLE POL_NEG CUI_0020405R SMG_TITLE T R T R Title: Reactive arthritis developing after pneumococcal conjunctivitis: a case report | Journal of Medical Case Reports | Full Text DOI: 10.1186/1752-1947-1-2 Abstract Background S. pneumoniae is a known cause of bacterial conjunctivitis and can be transmitted through contact with infected carriers. Case presentation A 38-year-old ophthalmologist developing reactive arthritis following clinic-acquired pneumococcal conjunctivitis.

For Users No changes required if you don t want to use new features User interface is updated, so will take some learning We think it should be easier to use Many more features previously hidden are now exposed No more using ^ to denote case sensitive searches Proximity searches Exclude phrase is now better integrated Exclude notes is now easily available Better checking of terms for potential problems Search terms shown in original form, making it easier to interpret (although some characters are ignored) s p and is now s/p AND Additional interface enhancements for more clarity (moving some buttons to more logical locations) Upcoming

For Users Can now search by terms (words) or concept unique identifiers (CUIs), or a mix of both NLP enables searching with additional annotations such as negation Our most requested feature over the years Example, search for headache, but exclude denies headache When reviewing notes: highlight based on some NLP semantic groups drugs, anatomy, disorders, procedures, etc. Underline based on annotations negation, uncertainty, history of, etc. With filters, can search based on document date and/or age of patient at the time the document was created Query Details show logical AND/OR relationship which previously was not obvious to users Upcoming

For Users One Implication of the change: Standard term entry is now more powerful/capable than Advanced Terms . Only exception (for now) is better control over Boolean searching when using Advanced Terms Upcoming